Injustice has often been a result of the way power was distributed, not metaphysical beliefs. In the Soviet Union, the Bolsheviks were arch-atheists who assessed Christianity as an enemy to be destroyed, expressed by Vladimir Lenin and other Soviet leaders: "Our revolution will never succeed until the myth of God is removed from the mind of man."
Lenin (Chairman of the Council) was succeeded by Alexei Rykov (Joseph Stalin as the party leader). Estimates of how many people died in Stalin's engineered famine of 1933 vary. But they are staggering in their scale -- between 3 and 7 million people.
The atheist agenda of the Soviet Union didn't necessarily do any good for the nation and its people in itself.
The reason why Stalin starved the citizens that lived in Ukrain is because they wanted to secede, he viewed this as a political threat, so he just did away with them. The theocratic monarchies in medieval Europe also mainly persecuted people with counter religious or political ideologies because it threatened their empire.
The communist political system under Stalin was different than the absolute theocratic monarchies in medieval Europe but it was still a totalitarian government. Communist states do not have a separation of powers; instead, they have one national legislative body (such as the Supreme Soviet in the Soviet Union) which is considered the highest organ of state power and which is legally superior to the executive and judicial branches of government. To achieve his goals, Stalin created a new kind of government, a totalitarian state. In a totalitarian state, the government is a single-party dictatorship that controls every aspect of the lives of its citizens.
I've read a lot of the Christian Greek scriptures. Nowhere does it say that Jesus or any of his apostles killed people or sought to kill people for any reason and the Humanist Manifesto (while somewhat contemporary) doesn't have any chapters or verses that incite violence. When power is in the hands of just a few (dictatorships, monarchies) the abuse of power is generally what follows.